Emerging hardware devices (e.g., NVMe SSD, RISC-V, etc.) open new opportunities for improving the overall performance of computer systems. In addition, the applications try to fully utilize hardware resources to keep up with those improvements. However, these trends can cause significant file system overheads (i.e., fragmentation issues). In this paper, we first study the reason for the fragmentation issues on an F2FS file system and present a new tool, called FragTracer, which helps to analyze the ratio of fragmentation in real-time. For user-friendly usage, we designed FragTracer with three main modules, monitoring, pre-processing, and visualization, which automatically runs without any user intervention. We also optimized FragTracer in terms of performance to hide its overhead in tracking and analyzing fragmentation issues on-the-fly. We evaluated FragTracer with three real-world databases on the F2FS file system, so as to study the fragmentation characteristics caused by databases, and we compared the overhead of FragTracer. Our evaluation results clearly show that the overhead of FragTracer is negligible when running on commodity computing environments.